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/*
* $Id$
* $URL$
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2016 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
*
* This library is free software; you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as .
* ----------------------------------------------------------------------------
*/
package org.sbml.jsbml.ext.layout;
import java.text.MessageFormat;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.Reaction;
/**
* Analogous to how a {@link Reaction} object has to at least have one reactant
* or product, the {@link ReactionGlyph} has to at least have one
* {@link SpeciesReferenceGlyph} stored in the
* {@link #listOfSpeciesReferencesGlyphs}. The {@link ReactionGlyph} inherits
* from {@link GraphicalObject}.
* In addition to the attributes inherited from {@link GraphicalObject}, the
* {@link ReactionGlyph} is described by an attribute reaction, a {@link Curve}
* element and a {@link #listOfSpeciesReferencesGlyphs} element.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @since 1.0
* @version $Rev$
*/
public class ReactionGlyph extends AbstractReferenceGlyph {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 8770691813350594995L;
/**
*
*/
private Curve curve;
/**
*
*/
private ListOf listOfSpeciesReferencesGlyphs;
/**
*
*/
public ReactionGlyph() {
super();
initDefaults();
}
/**
*
* @param level
* @param version
*/
public ReactionGlyph(int level, int version) {
super(level, version);
initDefaults();
}
/**
*
* @param reactionGlyph
*/
public ReactionGlyph(ReactionGlyph reactionGlyph) {
super(reactionGlyph);
if (reactionGlyph.isSetCurve()) {
setCurve(reactionGlyph.getCurve().clone());
}
if (reactionGlyph.isSetListOfSpeciesReferencesGlyphs()) {
setListOfSpeciesReferencesGlyph(reactionGlyph
.getListOfSpeciesReferenceGlyphs().clone());
}
}
/**
*
* @param id
*/
public ReactionGlyph(String id) {
super(id);
initDefaults();
}
/**
*
* @param id
* @param level
* @param version
*/
public ReactionGlyph(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/**
* Initializes the default values using the namespace.
*/
@Override
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/**
* Appends the specified element to the end of the
* {@link #listOfSpeciesReferencesGlyphs}.
*
* @param glyph
* @return {@code true} (as specified by {@link Collection#add})
* @throws NullPointerException
* if the specified element is null and this list does not
* permit null elements
* @throws IllegalArgumentException
* if some property of this element prevents it from being added
* to this list
*/
public boolean addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph) {
return getListOfSpeciesReferenceGlyphs().add(glyph);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#clone()
*/
@Override
public ReactionGlyph clone() {
return new ReactionGlyph(this);
}
/**
* Creates and adds a new {@link Curve} to this ReactionGlyph.
*
* @return a new {@link Curve} instance.
*/
public Curve createCurve() {
Curve newcurve = new Curve(getLevel(), getVersion());
setCurve(newcurve);
return newcurve;
}
/**
* Creates and adds a new {@link SpeciesReferenceGlyph}
*
* @param id the identifier for the {@link SpeciesReferenceGlyph} to be created.
* @return a new {@link SpeciesReferenceGlyph}.
*/
public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id) {
SpeciesReferenceGlyph glyph = new SpeciesReferenceGlyph(id, getLevel(), getVersion());
addSpeciesReferenceGlyph(glyph);
return glyph;
}
/**
* Creates and adds a new {@link SpeciesReferenceGlyph}
*
* @param id
* the identifier for the {@link SpeciesReferenceGlyph} to be created.
* @param speciesGlyph
* corresponding {@link SpeciesGlyph} ID.
* @return a new {@link SpeciesReferenceGlyph} that points to the given
* {@code speciesGlyph}.
*/
public SpeciesReferenceGlyph createSpeciesReferenceGlyph(String id, String speciesGlyph) {
SpeciesReferenceGlyph glyph = createSpeciesReferenceGlyph(id);
glyph.setSpeciesGlyph(speciesGlyph);
return glyph;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
if (equals) {
ReactionGlyph reactionGlyph = (ReactionGlyph) object;
equals &= reactionGlyph.isSetCurve() == isSetCurve();
if (equals && isSetCurve()) {
equals &= reactionGlyph.getCurve().equals(getCurve());
}
equals &= reactionGlyph.isSetListOfSpeciesReferencesGlyphs() == isSetListOfSpeciesReferencesGlyphs();
if (equals && isSetListOfSpeciesReferencesGlyphs()) {
equals &= reactionGlyph.getListOfSpeciesReferenceGlyphs().equals(getListOfSpeciesReferenceGlyphs());
}
}
return equals;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#getChildAt(int)
*/
@Override
public TreeNode getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(Integer.toString(index));
}
int count = super.getChildCount(), pos = 0;
if (index < count) {
return super.getChildAt(index);
} else {
index -= count;
}
if (isSetCurve()) {
if (pos == index) {
return getCurve();
}
pos++;
}
if (isSetListOfSpeciesReferencesGlyphs()) {
if (pos == index) {
return getListOfSpeciesReferenceGlyphs();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#getChildCount()
*/
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetCurve()) {
count++;
}
if (isSetListOfSpeciesReferencesGlyphs()) {
count++;
}
return count;
}
/**
*
* @return
*/
public Curve getCurve() {
return curve;
}
/**
* If the {@link #listOfSpeciesReferencesGlyphs} has not yet been initialized, this
* will be done by this method.
*
* @return the {@link #listOfSpeciesReferencesGlyphs}
*/
public ListOf getListOfSpeciesReferenceGlyphs() {
if (!isSetListOfSpeciesReferencesGlyphs()) {
listOfSpeciesReferencesGlyphs = new ListOf();
listOfSpeciesReferencesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesReferencesGlyphs.setPackageName(null);
listOfSpeciesReferencesGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfSpeciesReferencesGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfSpeciesReferencesGlyphs);
}
return listOfSpeciesReferencesGlyphs;
}
/**
*
* @return
*/
public String getReaction() {
return getReference();
}
/**
* Note that the return type of this method is {@link NamedSBase} because it
* could be possible to link some element from other packages to this glyph.
*
* @return
*/
public NamedSBase getReactionInstance() {
return getNamedSBaseInstance();
}
/**
*
* @param i
* @return
*/
public SpeciesReferenceGlyph getSpeciesReferenceGlyph(int i) {
return getListOfSpeciesReferenceGlyphs().get(i);
}
/**
*
* @param srGlyphId
* @return
*/
public SpeciesReferenceGlyph getSpeciesReferenceGlyph(String srGlyphId) {
return getListOfSpeciesReferenceGlyphs().firstHit(new NamedSBaseReferenceFilter(srGlyphId));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 953;
int hashCode = super.hashCode();
if (isSetCurve()) {
hashCode += prime * getCurve().hashCode();
}
if (isSetListOfSpeciesReferencesGlyphs()) {
hashCode += prime * getListOfSpeciesReferenceGlyphs().hashCode();
}
return hashCode;
}
/**
* @return
*/
public boolean isSetCurve() {
return curve != null;
}
/**
* @return
*/
public boolean isSetListOfSpeciesReferencesGlyphs() {
return listOfSpeciesReferencesGlyphs != null;
}
/**
* @return
*/
public boolean isSetReaction() {
return isSetReference();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix,
String value) {
boolean isAttributeRead = super.readAttribute(attributeName, prefix,
value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals("reaction")) {
setReaction(value);
} else {
return false;
}
}
return isAttributeRead;
}
/**
* The curve describes the center section of a {@link ReactionGlyph}. The center
* section is frequently used by tools to separate the point where substrates arcs come together
* from the point where product arcs split off. The {@link Curve} is optional, and when not present
* the dimensions of the inherited {@link BoundingBox} describes the center section, by storing its
* position and dimension.
*
* @param curve
*/
public void setCurve(Curve curve) {
if (this.curve != null) {
Curve oldValue = this.curve;
this.curve = null;
oldValue.fireNodeRemovedEvent();
}
this.curve = curve;
registerChild(this.curve);
}
/**
* Since the {@link Species} element can have several graphical representations
* in the layout there must be a way to specify which {@link SpeciesGlyph} should
* be connected to the {@link ReactionGlyph}. This is done using the
* listOfSpeciesReferenceGlyphs.
*
* @param listOfSpeciesReferencesGlyph
*/
public void setListOfSpeciesReferencesGlyph(ListOf listOfSpeciesReferencesGlyph) {
unsetListOfSpeciesReferencesGlyph();
listOfSpeciesReferencesGlyphs = listOfSpeciesReferencesGlyph;
if (listOfSpeciesReferencesGlyphs != null) {
listOfSpeciesReferencesGlyphs.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'layout'
listOfSpeciesReferencesGlyphs.setPackageName(null);
listOfSpeciesReferencesGlyphs.setPackageName(LayoutConstants.shortLabel);
listOfSpeciesReferencesGlyphs.setSBaseListType(ListOf.Type.other);
registerChild(listOfSpeciesReferencesGlyphs);
}
}
/**
* See setReaction(String)
*
* @param reaction
*/
public void setReaction(Reaction reaction) {
setReaction(reaction.getId());
}
/**
* The reaction attribute is used to specify the id of the corresponding
* {@link Reaction} in the {@link Model}. This reference is optional.
*
* @param reaction
*/
public void setReaction(String reaction) {
setReference(reaction, LayoutConstants.reaction);
}
/**
*
*/
public void unsetListOfSpeciesReferencesGlyph() {
if (listOfSpeciesReferencesGlyphs != null) {
ListOf oldValue = listOfSpeciesReferencesGlyphs;
listOfSpeciesReferencesGlyphs = null;
oldValue.fireNodeRemovedEvent();
}
}
/**
*
*/
public void unsetReaction() {
unsetReference();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetReaction()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.reaction, getReaction());
}
return attributes;
}
}
